Germplasm Groups Research Articles

Efficiency of phenotypic and DNA markers for a genetic diversity study of alfalfa

Information on genetic diversity and germplasm characterization is essential for successful crop improvement. Diverse data sets (pedigree, morphological, biochemical, DNA based-markers) are employed in various aspects of plant analysis. The objective of this study was to determine the efficiency of phenotypic and RAPD markers in diversity assessment often alfalfa (Medicago spp.) accessions from Europe, North America and Australia. Field experiment was designed as a randomised complete block with three replications over two consecutive years (2004, 2005) at one location. Twelve morpho-agronomic traits were recorded on 50 plants per each accession. Genomic DNA's from 16-20 randomly selected individual plants per accession were used for RAPD analysis. Six primers selected in this study generated a total of 93 polymorphic RAPD bands. The number of polymorphic bands detected per primer ranged from 11 to 20. Genetic distances (GD) among investigated accessions and two-dimensional principal coordinate analysis (2D PCoA) based on phenotypic and molecular data were obtained. The average GD between (0.283-0.416) and within (0.247-0.332) accessions based on RAPD data was higher than GD values obtained by morpho-agronomic traits (0.171-0.354 and 0.157-0.261, respectively). 2D PCoA based on GD from RAPD data grouped most of the studied individual plants to four clusters according to their geographical or taxonomy origin. 2D PCoA based only on morpho-agronomic data did not group plants congruently to their origin, probably due to a strong environmental influence on studied traits. Our results indicated that the RAPD markers were effective in assessing genetic diversity within and between studied alfalfa accessions. In addition, the obtained results suggested that the RAPD markers might be useful for grouping of germplasm with similar genetic background and for prescreening of potential heterotic groups in our breeding programme.

Variability in four diverse cotton (Gossypium hirsutum L.) germplasm populations

A broad range of cotton (Gossypium hirsutum L.) germplasm resources exist with characteristics useful for improving modern cotton cultivars. However, much of this germplasm is not well utilized. The objective of this study was to evaluate agronomic and fiber traits of four germplasm populations to determine the effectiveness of pooling germplasm for generating variability to improve traits of interest. Four populations were developed with parents chosen based on (1) dwarfing genes, (2) a combination of fiber strength and length traits, (3) glandless genes, or (4) inclusion in the G. hirsutum center-of-origin, i.e. race, germplasm group. The dwarf germplasm population had smaller bolls, a smaller lint index, a smaller seed index, lower micronaire, and shorter fibers than the other three populations. There were no significant differences in lint yield, elongation, or strength among the germplasm populations. In contrast to the general lack of significant differences among populations for agronomic and fiber traits, within population variation was observed to be high. Therefore, selections could be made within the race population to raise lint yields and within the fiber population to increase fiber length. Likewise, selections within the glandless population could be made for boll size, lint index, seed index, micronaire, and strength. These results suggest that intercrossing multiple parents in complex populations generates a large amount of variability with potential uses in crop improvement.

Combining the yield ability and secondary traits of selected cassava genotypes in the semi-arid areas of Eastern Kenya

effects (57 to 75%) explained variation for shoot weight, root weight, harvest index, dry matter content, root cyanide content and resistance to cassava mosaic, while GCA effects (55%) were more important for root number. Thus, our results suggested that non-additive gene action was more important than additive gene action in influencing yield and most of its associated traits in this cassava population. Overall, the results suggested that the success of cassava breeding in the semi-arid areas would depend on the ability of breeders to assemble heterotic groups of germplasm that combine well in order to achieve early vigour, disease and pest resistance, root quality and high yield potential.

Interspecies and intergenus transferability of barley and wheat D‐genome microsatellite markers

A selection of 147 wheat D‐genome and 130 barley genomic simple sequence repeat (gSSR) markers were screened for their utility in Hordeum chilense, as an alien donor genome for cereal breeding. Fifty‐eight wheat D‐genome and 71 barley PCR primer pairs consistently amplified products from H. chilense. Nineteen wheat D‐genome and 20 barley gSSR markers were polymorphic and allowed wide genome coverage of the H. chilense genome. Twenty‐three of the wheat D‐genome and 11 barley PCR primer pairs were suitable for studying the introgressions of H. chilense into wheat, amplifying H. chilense products of distinct size. In 88% of the markers tested, H. chilense products were maintained in the expected homeologous linkage group, as revealed by the analysis of wheat/H. chilense addition lines. Twenty‐nine microsatellite markers (eight gSSRs and 21 expressed sequence tags‐SSRs) uniformly distributed across the genome were tested for their utility in genetic diversity analysis within the species. Three genetic clusters are reported, in accordance with previous morphological and amplified fragment length polymorphism data. These results show that it is possible to discriminate the three previously established germplasm groups with microsatellite markers. The reported markers represent a valuable resource for the genetic characterisation of H. chilense, for the analysis of its genetic variability, and as a tool for wheat introgression. This is the first intraspecific study in a collection of H. chilense germplasm using microsatellite markers.

Transcriptome-based distance measures for grouping of germplasm and prediction of hybrid performance in maize

Grouping of germplasm and prediction of hybrid performance and heterosis are important applications in hybrid breeding programs. Gene expression analysis is a promising tool to achieve both tasks efficiently. Our objectives were to (1) investigate distance measures based on transcription profiles, (2) compare these with genetic distances based on AFLP markers, and (3) assess the suitability of transcriptome-based distances for grouping of germplasm and prediction of hybrid performance and heterosis in maize. We analyzed transcription profiles from seedlings of the 21 parental maize lines of a 7 x 14 factorial with a 46-k oligonucleotide array. The hybrid performance and heterosis of the 98 hybrids were assessed in field trials. In cluster and principal coordinate analyses for germplasm grouping, the transcriptome-based distances were as powerful as the genetic distances for separating flint from dent inbreds. Cross validation showed that prediction of hybrid performance with transcriptome-based distances using selected markers was more precise than earlier prediction models using DNA markers or general combining ability estimates using field data. Our results suggest that transcriptome-based prediction of hybrid performance and heterosis has a great potential to improve the efficiency of maize hybrid breeding programs.

Wide variability in kernel composition, seed characteristics, and zein profiles among diverse maize inbreds, landraces, and teosinte

All crop species have been domesticated from their wild relatives, and geneticists are just now beginning to understand the consequences of artificial (human) selection on agronomic traits that are relevant today. The primary consequence is a basal loss of diversity across the genome, and an additional reduction in diversity for genes underlying traits targeted by selection. An understanding of attributes of the wild relatives may provide insight into target traits and valuable allelic variants for modern agriculture. This is especially true for maize (Zea mays ssp. mays), where its wild ancestor, teosinte (Z. mays ssp. parviglumis), is so strikingly different than modern maize. One obvious target of selection is the size and composition of the kernel. We evaluated kernel characteristics, kernel composition, and zein profiles for a diverse set of modern inbred lines, teosinte accessions, and landraces, the intermediate between inbreds and teosinte. We found that teosinte has very small seeds, but twice the protein content of landraces and inbred lines. Teosinte has a higher average alpha zein content (nearly 89% of total zeins as compared to 72% for inbred lines and 76% for landraces), and there are many novel alcohol-soluble proteins in teosinte relative to the other two germplasm groups. Nearly every zein protein varied in abundance among the germplasm groups, especially the methionine-rich delta zein protein, and the gamma zeins. Teosinte and landraces harbor phenotypic variation that will facilitate genetic dissection of kernel traits and grain quality, ultimately leading to improvement via traditional plant breeding and/or genetic engineering.

Peanut Aflatoxin and Genomics Research in China: Progress and Perspectives

Abstract Peanut is an important oil and food crop in China with a unique role in agricultural development and food security. Aflatoxin contamination in peanut, normally more serious in southern parts of the country, is a crucial factor affecting sustainable development of the peanut industry. Extensive efforts have been made at several institutions in China for aflatoxin management and related genomics research. Several local peanut germplasm lines have been identified as resistant to seed infection by Aspergillus flavus or aflatoxin production. Two AFLP markers have been identified that are linked with resistance to seed invasion and one was converted into a SCAR marker for more efficient breeding application. Several new peanut cultivars with improved productivity and possessing resistance to aflatoxin contamination are extensively used in production. Integrated management approaches have been recommended to farmers based on agro-ecological characteristics in different regions. More recently, molecular techniques have been extensively used in genetic diversity assessment, investigation of genetic relationships among different germplasm groups, marker development, identification of interspecific genome introgression, gene cloning and function analysis, and genetic transformation of important traits concerning productivity, quality and food safety of peanut. Special emphasis has been placed on resistance to aflatoxin, bacterial wilt, foliar diseases and fatty acid desaturase. Perspectives of peanut genetic improvement and further research priorities are also discussed.

Genotypic identification and diversity evaluation of a sweet potato ( Ipomoea batatas (L). Lam) collection using microsatellites

Characterization and genotype identification are essential for rational conservation, management and genetic diversity evaluation. In this work, simple sequence repeat (SSR) markers were used to identify 57 accessions of sweet potato kept at the ‘in vitro’ Gene Bank of INTA, Argentina. This collection includes primitive materials from primary zones of dispersion, commercial varieties, breeding clones and foreign materials from different parts of the world (Africa, Asia and USA). Average similarity between the materials evaluated was 0.367. Grouping analysis revealed six clusters and a strong association with skin colour of storage roots. The set of selected SSR markers allowed us to verify identity, detect duplicates and estimate the genetic similarity of the materials analysed. This characterization complements morphological data and provides tools to estimate the variation of diversity between local and foreign germplasm groups.

A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica–japonica hybrids in rice

Hybrid sterility is a major form of postzygotic reproductive isolation. Although reproductive isolation has been a key issue in evolutionary biology for many decades in a wide range of organisms, only very recently a few genes for reproductive isolation were identified. The Asian cultivated rice (Oryza sativa L.) is divided into two subspecies, indica and japonica. Hybrids between indica and japonica varieties are usually highly sterile. A special group of rice germplasm, referred to as wide-compatibility varieties, is able to produce highly fertile hybrids when crossed to both indica and japonica. In this study, we cloned S5, a major locus for indica-japonica hybrid sterility and wide compatibility, using a map-based cloning approach. We show that S5 encodes an aspartic protease conditioning embryo-sac fertility. The indica (S5-i) and japonica (S5-j) alleles differ by two nucleotides. The wide compatibility gene (S5-n) has a large deletion in the N terminus of the predicted S5 protein, causing subcellular mislocalization of the protein, and thus is presumably nonfunctional. This triallelic system has a profound implication in the evolution and artificial breeding of cultivated rice. Genetic differentiation between indica and japonica would have been enforced because of the reproductive barrier caused by S5-i and S5-j, and species coherence would have been maintained by gene flow enabled by the wide compatibility gene.

Allele Sequencing of the Barley Stem Rust Resistance Gene Rpg1 Identifies Regions Relevant to Disease Resistance

The stem rust resistance gene Rpg1 has protected North American barley cultivars from significant yield losses for over 65 years. The remarkable durability of this gene warrants further study as to its possible origin and allelic variation. Eight Swiss barley (Hordeum vulgare) landraces and eight wild barley (H. vulgare subsp. spontaneum) accessions from diverse geographic regions were analyzed to uncover new alleles of Rpg1 and learn about its possible origin. The two germplasm groups included accessions that were resistant and susceptible to Puccinia graminis f. sp. tritici pathotype MCCF. Allele-specific primers were utilized to amplify 1 kbp overlapping fragments spanning the Rpg1 gene and sequenced if a polymerase chain reaction (PCR) fragment was generated. Variation among the PCR products revealed significant polymorphisms among these Hordeum accessions. Landraces and wild barley accessions susceptible to pathotype MCCF exhibited the highest degree of Rpg1 polymorphism. One resistant landrace (Hv672) and one resistant wild barley accession (WBDC040) yielded all seven Rpg1-specific PCR fragments, but only landrace Hv672 coded for an apparently functional Rpg1 as determined by comparison to previously characterized resistant and susceptible alleles and also resistance to HKHJ, a stem rust pathotype that can specifically detect Rpg1 in the presence of other resistance genes. Accessions resistant to stem rust pathotype MCCF, but completely lacking Rpg1-specific PCR amplification and hybridization with an Rpg1-specific probe, suggested the presence of stem rust resistant gene(s) different from Rpg1 in the Hordeum germplasm pool. Some Rpg1 alleles that retained the ability to autophosphorylate did not confer resistance to Puccinia graminis f. sp. tritici pathotype MCCF, confirming our previous observations that autophosphorylation is essential, but not sufficient for disease resistance. Thus, the RPG1 protein plays a complex role in the stem rust disease resistance-signaling pathway.

Molecular characterization of an international cacao collection using microsatellite markers

Plant germplasm collections invariably contain varying levels of genetic redundancy, which hinders the efficient conservation and utilization of plant germplasm. Reduction of genetic redundancies is an essential step to improve the accuracy and efficiency of genebank management. The present study targeted the assessment of genetic redundancy and genetic structure in an international cacao (Theobroma cacao L.) collection maintained in Costa Rica. A total of 688 cacao accessions maintained in this collection were genotyped with 15 simple sequence repeat (SSR) loci, using a capillary electrophoresis genotyping system. The SSR markers provided a high resolution among the accessions. Thirty-six synonymously labeled sets, involving 135 accessions were identified based on the matching of multilocus SSR profiles. After the elimination of synonymous sets, the level of redundancy caused by closely related accessions in the collection was assessed using a simulated sampling scheme that compared allelic diversity in different sample sizes. The result of the simulation suggested that a random sample of 113 accessions could capture 90% of the total allelic diversity in this collection. Principal Coordinate Analysis revealed that the Trinitario hybrids from Costa Rica shared a high similarity among groups as well as among individual accessions. The analysis of the genetic structure illustrated that the within-country/within-region difference accounted for 84.6% of the total molecular variation whereas the among-country/among-region difference accounted for 15.4%. The Brazilian germplasm contributed most to this collection in terms of total alleles and private alleles. The intercountry/interregion relationship by cluster analysis largely agreed with the geographical origin of each germplasm group and supported the hypothesis that the Upper Amazon region is the center of diversity for cacao. The results of the present study indicated that the CATIE International Cacao Collection contains a high level of genetic redundancy. It should be possible to rationalize this collection by reducing redundancy and ensuring optimal representation of the genetic diversity from distinct germplasm groups. The results also demonstrated that SSR markers, together with the statistical tools for individual identification and redundancy assessment, are technically practical and sufficiently informative to assist the management of a tropical plant germplasm collection.

Genotypic variations in activities of phosphoenolpyruvate carboxylase and correlations with leaf photosynthetic characteristics and crop productivity of cassava grown in low-land seasonally-dry tropics

Field trials with a large group of cassava germplasm were conducted at the seasonally-dry and hot environments in southwest Colombia to investigate photosynthetic characteristics and production under drought conditions. Measurement of net photosynthetic rate (P N), photosynthetic nitrogen use efficiency (PNUE), mesophyll conductance to CO2 diffusion (g m), and phosphoenolpyruvate carboxylase (PEPC) activity of upper canopy leaves were made in the field. All photosynthetic characteristics were significantly correlated with final dry root yield (Yield). Correlations among the photosynthetic traits were also significant. PEPC activity was highly significantly correlated with P N and PNUE, indicating the importance of the enzyme in cassava photosynthesis and productivity. Among a small selected group from the preliminary trial for yield performance, the second year Yield was highly significantly correlated with P N measured on the first year crop. Thus variations in the measured photosynthetic traits are genetically controlled and underpin variations in yield. One short-stemmed cultivar M Col 2215 was selected for high root dry matter content, high harvest index, and tolerance to drought. It was tested under the semi-arid conditions of the west coast of Ecuador; participating farmers evaluated cultivar performance. This cultivar was adopted by farmers and officially released in 1992 under the name Portoviejo 650.

Tracing the Geographic Origins of Major Avocado Cultivars

It has been difficult to infer the genetic history of avocado breeding, owing to the role of hybridization in the origin of contemporary avocado cultivars. To address this difficulty, we used the model-based clustering program, STRUCTURE, and nucleotide polymorphism in 5960 bp of sequence from 4 nuclear loci to examine population structure in 21 wild avocado accessions. The origins of 33 cultivars were inferred relative to the wild sample. Nucleotide sequence diversity in domesticated avocados ranged between 80% and 90% of that observed for the same loci in wild avocado, depending on the diversity statistic used for comparison. Substantial genetic differentiation among 3 geographic groups of wild germplasm corresponded to the classically defined horticultural races of avocado. Previously undetected genetic differentiation was revealed in wild populations from Central Mexico, where 2 subpopulations were distinguished based on elevation and latitude.

Assessment of different genetic distances in constructing cotton core subset by genotypic values

One hundred and sixty-eight genotypes of cotton from the same growing region were used as a germplasm group to study the validity of different genetic distances in constructing cotton core subset. Mixed linear model approach was employed to unbiasedly predict genotypic values of 20 traits for eliminating the environmental effect. Six commonly used genetic distances (Euclidean, standardized Euclidean, Mahalanobis, city block, cosine and correlation distances) combining four commonly used hierarchical cluster methods (single distance, complete distance, unweighted pair-group average and Ward's methods) were used in the least distance stepwise sampling (LDSS) method for constructing different core subsets. The analyses of variance (ANOVA) of different evaluating parameters showed that the validities of cosine and correlation distances were inferior to those of Euclidean, standardized Euclidean, Mahalanobis and city block distances. Standardized Euclidean distance was slightly more effective than Euclidean, Mahalanobis and city block distances. The principal analysis validated standardized Euclidean distance in the course of constructing practical core subsets. The covariance matrix of accessions might be ill-conditioned when Mahalanobis distance was used to calculate genetic distance at low sampling percentages, which led to bias in small-sized core subset construction. The standardized Euclidean distance is recommended in core subset construction with LDSS method.

Tall Fescue Adaptation to Low Nitrogen Fertilization in Relation to Germplasm Type and Endophyte Infection

Efficient crop growth with low nitrogen (N) application is becoming a requirement to face the concern on excessive N emission to the environment and the increasing cost of fertilizers. This study compared six natural populations and three improved varieties of tall fescue (Festuca arundinacea Schreb.) for dry-matter yield over 4 years under ordinary N fertilization (450 kg ha−1 in the 4 years) and very low N fertilization (only 40 kg ha−1 prior to sowing). Both endophyte-infected (EI) and endophyte-free (EF) forms of each accession were sown. On average, ordinary fertilization implied 30 % higher yield than very low fertilization and the EI germplasm outyielded the corresponding EF germplasm (+4.4 %). Mean yield of improved varieties was higher than that of natural populations under ordinary fertilization (P < 0.05), whereas the two germplasm groups did not differ under very low fertilization. Accession × N fertilization interaction was found among natural populations but not among varieties (P < 0.05). A few natural populations were top-yielding under very low fertilization and may be exploited, possibly in combination with endophyte infection, to select tall fescue varieties with enhanced performance under limited N application.

Genetic Diversity in CIMMYT Nontemperate Maize Germplasm: Landraces, Open Pollinated Varieties, and Inbred Lines

CIMMYT is the source of improved maize (Zea mays L.) breeding material for a significant portion of the nontemperate maize growing world. Landraces which did not serve as sources for improved maize germplasm may contain untapped allelic variation useful for future breeding progress. Information regarding levels of diversity in different germplasm would help to identify sources for broadening improved breeding pools and in seeking genes and alleles that have not been tapped in modern maize breeding. The objectives of this study were to examine the diversity in maize landraces, modern open pollinated varieties (OPVs), and inbred lines adapted to nontemperate growing areas to find unique sources of allelic diversity that may be used in maize improvement. Twenty‐five simple sequence repeat markers were used to characterize 497 individuals from 24 landraces of maize from Mexico, 672 individuals from 23 CIMMYT improved breeding populations, and 261 CIMMYT inbred lines. Number of alleles, gene diversity per locus, unique alleles per locus, and population structure all differ between germplasm groups. The unique alleles found in each germplasm group represent a great reservoir of untapped genetic resources for maize improvement, and implications for hybrid breeding are discussed.

Consequences of a decentralized participatory barley breeding programme on changes in SSR allele frequency and diversity in one cycle of selection

AbstractChanges in allele type, allele frequency and genetic diversity because of selection by individual farmers and breeders were assessed using simple sequence repeats (SSRs) during one cycle of selection in a decentralized participatory barley breeding programme. Selection by both breeders and farmers resulted in the loss of a number of alleles in the majority of the locations, with more alleles lost in the heterogeneous breeding materials than in the fixed genotypes, indicating selection against undesirable traits uncovered in the heterogeneous breeding materials that are presumably linked to SSR alleles. After selection, significant allelic frequency changes were observed at several loci in both the germplasm groups. As the selection was conducted independently in each location, an allele had a chance of being selected in more than one location, and therefore considering the whole study area the allelic composition and diversity of the original genetic materials was maintained after the selection. The study showed the importance of decentralized participatory plant breeding in maintaining genetic diversity that helps stabilize and sustain production in unpredictable production conditions.

Microsatellite variation and population structure in the “Refractario” cacao of Ecuador

Utilization of germplasm for crop improvement is often hampered by absence of information regarding origin, genetic identity and genealogical relationships of germplasm groups or populations. Molecular marker technology offers an efficient tool to verify or reconstruct passport data. Using a high-throughput genotyping system with 15 microsatellite loci, we fingerprinted 482 accessions in 48 putative half-sib families of Refractario cacao (a group of germplasm collected from nine farms in Ecuador). Based on the multilocus profiles, a Bayesian method for individual assignment was applied to verify membership in each half-sib family. Multivariate statistical analysis showed that the Refractario genetic profile was different from other groups tested, except for the “Nacional” cacao from the coastal valley of Ecuador. Hierarchical partitioning of genetic variance in the Refractario cacao showed that 76% of the variation was contributed by intra-family difference, whereas the inter-family and inter-farm difference accounted for 15 and 9% of total variance, respectively. All three sources of variation were highly significant (P < 0.01). Cluster and Principal Coordinates Analyses revealed a population sub-structure in Refractario, which was also highly heterozygous, suggesting hybridization derived from Nacional cacao and multiple other parental varieties, which all shared a similar genetic background. The improved understanding of identities and structure in Refractario cacao will contribute to more efficient conservation and use of this germplasm group in cacao breeding.

Genetic structure and differentiation in hop (Humulus lupulus L.) as inferred from microsatellites

A set of 67 wild and cultivated hop accessions, representative of hop diversity, was genotyped with 29 SSR markers in order to investigate the population structure and genetic diversity among hop genotypes. A total of 314 alleles was detected, with an average of 10.8 alleles per locus and an average PIC content of 0.607. Model-based clustering placed the accessions into five germplasm groups. A distance-based tree showed good agreement with five germplasm groups, and additionally assigned accessions omitted from model-based analysis into two additional germplasm groups. The 67 hop accessions were thus subdivided in seven germplasm groups, with three corresponding to major breeding groups and four to wild hops. This finding is in accordance with two biogeographically separated hop germplasms (European and North American origin) and with the known history of the accessions. North American hop germplasm was partitioned into native and cultivated germplasm groups. European germplasm was divided into two groups of hop cultivars representing distinguishable European germplasms and three new groups of native hops, which were differentiated for the first time by this analysis. Admixture analysis showed shares of various ancestries in hop cultivars, mostly congruent with pedigree data, and the introgression of various ancestries in some native hops. The above results have so far given the most detailed insight to date into the population structure of hop diversity, which is important for its effective use in hop breeding.

Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations

Prospects for utilizing whole-genome association analysis in autogamous plant populations appear promising due to the reported high levels of linkage disequilibrium (LD). To determine the optimal strategies for implementing association analysis in soybean (Glycine max L. Merr.), we analyzed the structure of LD in three regions of the genome varying in length from 336 to 574 kb. This analysis was conducted in four distinct groups of soybean germplasm: 26 accessions of the wild ancestor of soybean (Glycine soja Seib. et Zucc.); 52 Asian G. max Landraces, the immediate results of domestication from G. soja; 17 Asian Landrace introductions that became the ancestors of North American (N. Am.) cultivars, and 25 Elite Cultivars from N. Am. In G. soja, LD did not extend past 100 kb; however, in the three cultivated G. max groups, LD extended from 90 to 574 kb, likely due to the impacts of domestication and increased self-fertilization. The three genomic regions were highly variable relative to the extent of LD within the three cultivated soybean populations. G. soja appears to be ideal for fine mapping of genes, but due to the highly variable levels of LD in the Landraces and the Elite Cultivars, whole-genome association analysis in soybean may be more difficult than first anticipated.